BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 11-24-2010, 10:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Epitope mapping of the phosphorylation motif of the HIV-1 protein Vpu bound to the se

Epitope mapping of the phosphorylation motif of the HIV-1 protein Vpu bound to the selective monoclonal antibody using TRNOESY and STD NMR spectroscopy.

Related Articles Epitope mapping of the phosphorylation motif of the HIV-1 protein Vpu bound to the selective monoclonal antibody using TRNOESY and STD NMR spectroscopy.

Biochemistry. 2004 Nov 23;43(46):14555-65

Authors: Gharbi-Benarous J, Bertho G, Evrard-Todeschi N, Coadou G, Megy S, Delaunay T, Benarous R, Girault JP

The conformational preferences of a 22-amino acid peptide (LIDRLIERAEDpSGNEpSEGEISA) that mimics the phosphorylated HIV-1-encoded virus protein U (Vpu) antigen have been investigated by NMR spectroscopy. Degradation of HIV receptor CD4 by the proteasome, mediated by the HIV-1 protein Vpu, is crucial for the release of fully infectious virions. Phosphorylation of Vpu at sites Ser52 and Ser56 on the DSGXXS motif is required for the interaction of Vpu with the ubiquitin ligase SCF(beta)(-TrCP) which triggers CD4 degradation by the proteasome. This motif is conserved in several signaling proteins known to be degraded by the proteasome. The interaction of the P-Vpu(41-62) peptide with its monoclonal antibody has been studied by transferred nuclear Overhauser effect NMR spectroscopy (TRNOESY) and saturation transfer difference NMR (STD NMR) spectroscopy. The peptide was found to adopt a bend conformation upon binding to the antibody; the peptide residues (Asp51-pSer56) forming this bend are recognized by the antibody as demonstrated by STD NMR experiments. The three-dimensional structure of P-Vpu(41-62) in the bound conformation was determined by TRNOESY spectra; the peptide adopts a compact structure in the presence of mAb with formation of several bends around Leu45 and Ile46 and around Ile60 and Ser61, with a tight bend created by the DpS(52)GNEpS(56) motif. STD NMR studies provide evidence for the existence of a conformational epitope containing tandem repeats of phosphoserine motifs. The peptide's epitope is predominantly located in the large bend and in the N-terminal segment, implicating bidentale association. These findings are in excellent agreement with a recently published NMR structure required for the interaction of Vpu with the SCF(beta)(-TrCP) protein.

PMID: 15544326 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping.
Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping. Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping. Chem Biol Drug Des. 2010 Sep 1;76(3):218-33 Authors: Begley DW, Zheng S, Varani G Solution-state nuclear magnetic resonance (NMR) is a versatile tool for the study of binding interactions between small molecules and macromolecular targets. We applied ligand-based NMR techniques to the study of human thymidylate synthase (hTS) using known...
nmrlearner Journal club 0 01-05-2011 09:51 PM
[NMR paper] Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross-
Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross-saturation. Related Articles Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross-saturation. Biochemistry. 2005 Jan 18;44(2):518-23 Authors: Morgan WD, Frenkiel TA, Lock MJ, Grainger M, Holder AA We have applied NMR cross-saturation with TROSY detection to the problem of precisely mapping conformational epitopes on complete protein antigen molecules. We have investigated complexes of the Fab fragments of two antibodies that...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion
Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements. Related Articles Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements. J Am Chem Soc. 2004 Nov 3;126(43):14258-66 Authors: Lucas LH, Price KE, Larive CK It is important to characterize drug-albumin binding during drug discovery and lead optimization as strong binding may reduce bioavailability and/or increase the drug's in vivo half-life. Despite knowing about the location of human serum albumin (HSA)...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] NMR studies of the phosphorylation motif of the HIV-1 protein Vpu bound to the F-box
NMR studies of the phosphorylation motif of the HIV-1 protein Vpu bound to the F-box protein beta-TrCP. Related Articles NMR studies of the phosphorylation motif of the HIV-1 protein Vpu bound to the F-box protein beta-TrCP. Biochemistry. 2003 Dec 23;42(50):14741-51 Authors: Coadou G, Gharbi-Benarous J, Megy S, Bertho G, Evrard-Todeschi N, Segeral E, Benarous R, Girault JP A protein-protein association regulated by phosphorylation of serine is examined by NMR studies. Degradation of the HIV receptor CD4 by the proteasome, mediated by the HIV-1...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer diff
Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments. Related Articles Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments. Glycobiology. 2003 Jun;13(6):435-43 Authors: Rinnbauer M, Ernst B, Wagner B, Magnani J, Benie AJ, Peters T A complex between sialyl Lewisx (alpha-D-Neu5Ac-- beta-D-Gal---beta-D-GlcNAc-O-8 COOMe) and E-selectin was studied using saturation transfer difference (STD) nuclear magnetic resonance (NMR) experiments....
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Epitope mapping of ligand-receptor interactions by diffusion NMR.
Epitope mapping of ligand-receptor interactions by diffusion NMR. Related Articles Epitope mapping of ligand-receptor interactions by diffusion NMR. J Am Chem Soc. 2002 Aug 28;124(34):9984-5 Authors: Yan J, Kline AD, Mo H, Zartler ER, Shapiro MJ A novel method based on diffusion NMR for the epitope mapping of ligand binding is presented. The intermolecular NOE builds up during a long diffusion period and creates a deviation from the linearity. The ligand proton nearest the protein generates the strongest NOE from protein during the diffusion...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Group epitope mapping by saturation transfer difference NMR to identify segments of a
Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. Related Articles Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc. 2001 Jun 27;123(25):6108-17 Authors: Mayer M, Meyer B A protocol based on saturation transfer difference (STD) NMR spectra was developed to characterize the binding interactions at an atom level, termed group epitope mapping (GEM). As an example...
nmrlearner Journal club 0 11-19-2010 08:32 PM
Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping
Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping Peter Würtz, Olli Aitio, Maarit Hellman and Perttu Permi Journal of Biomolecular NMR; 2007; 39(2) pp 97 - 105 Abstract: Simultaneous recording of different NMR parameters is an efficient way to reduce the overall experimental time and speed up structural studies of biological macromolecules. This can especially be beneficial in the case of fast NMR-based drug screening applications or for collecting NOE restraints, where prohibitively long data collection...
stewart Journal club 0 08-05-2008 01:41 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 11:13 PM.


Map